* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Navigating the NCBI Intructions
Saethre–Chotzen syndrome wikipedia , lookup
Y chromosome wikipedia , lookup
Metagenomics wikipedia , lookup
Point mutation wikipedia , lookup
Human genome wikipedia , lookup
Gene therapy wikipedia , lookup
Gene expression profiling wikipedia , lookup
Pathogenomics wikipedia , lookup
Neocentromere wikipedia , lookup
Genetic engineering wikipedia , lookup
Public health genomics wikipedia , lookup
BRCA mutation wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Gene desert wikipedia , lookup
Gene nomenclature wikipedia , lookup
History of genetic engineering wikipedia , lookup
X-inactivation wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Gene expression programming wikipedia , lookup
Helitron (biology) wikipedia , lookup
Genome editing wikipedia , lookup
Oncogenomics wikipedia , lookup
Genome evolution wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Designer baby wikipedia , lookup
Microevolution wikipedia , lookup
Navigating the NCBI Instructions Aim: To become familiar with the resources available at the National Center for Bioinformatics (NCBI) and the search engine Entrez. Instructions: Write the answers to your questions on the Student Worksheet, in your lab notebook, or on a separate sheet of paper, as instructed by your teacher. 1. Go to the NCBI homepage http://www.ncbi.nih.gov/ Figure 1: Familiarize yourself with the NCBI homepage. Credit: NCBI. 2. Take a few minutes to look around the site. The goal is to familiarize yourself with a few key components of the NCBI. a. What is the name of one interesting resource or database shown in the blue box on the left? What do you think is its function or purpose? b. What is one interesting resource listed in the Popular Resources menu on the right? What do you think is its function or purpose? 3. Find the search box in the center of the webpage (black box in above image). This search box uses the NCBI search engine Entrez to look for your search term (or “query”) across all of the databases at the NCBI. Figure 2: Search for “BRCA1.” Credit: NCBI. 4. Type “BRCA1” into the Search box. Make sure there is no space between BRCA and 1. Click Search. BRCA1 is a tumor suppressor gene that normally prevents cancer. Mutations in this gene are associated with increased risk of hereditary breast cancer and ovarian cancer when normal function is lost. The white box to the left of each database contains the number of “hits” returned from that database (see screen shot, above). This is like searching in iTunes® without specifying categories like ringtones, podcasts, movies, TV, or songs. a. Why are we searching for BRCA1? b. The Nucleotide database has DNA sequences that have been loaded onto the NCBI database. How many times is ‘BRCA1’ cited in the Nucleotide database? c. The PubMed database has the articles that have been published about a specific gene or disease. How many times is ‘BRCA1’ cited in the PubMed database? d. Compare the numbers you got for Questions a and c. Do these relative numbers surprise you? What does this tell you about the BRCA1 gene? Explain. 5. Go back to the NCBI homepage by clicking the NCBI logo in the upper left corner of the screen. This search shows that there is a lot of i_n_f_o_r_m_a_t_i_o_n_ _a_t_ _t_h_e_ _N_C_B_I_!_ _I_t_ _c_a_n_ _b_e_ _c_h_a_l_l_e_n_g_i_n_g_ _t_o_ _t_r_y_ _t_o_ _m_a_k_e_ _s_e_n_s_e_ _o_f_ _i_t_ _a_l_l_._ _L_e_t_’s_ _s_t_a_r_t_ _w_i_t_h_ _s_o_m_e_t_h_i_n_g_ _m_o_r_e_ _f_a_m_i_l_iar_ 6. Click the “All Resources” link from the list of resources on the left side of the screen. Figure 3: Click “All Resources” on the left side of the screen. Credit: NCBI. 7. Find “Map Viewer.” Click on the “Tools” tab and either scroll through the alphabetical list, or use the “Find” feature (PC: “Control+F” Mac: “Command+F”) to Find “Map Viewer.” Click on the “Map Viewer” link. The resulting page is called Map Viewer and it allows us to search the genomes of many different organisms, including humans. Figure 4: Select “Homo sapiens” from the list of groups or organisms. Credit: NCBI. 8. Open the Search menu, select Homo sapiens from the pull-down menu, and click “Go.” 9. Now we can see the Homo sapiens (human) genome view. A genome is all of the genetic information in an organism. Each figure you see in the “genome view” represents a pair of chromosomes. Most of the chromosomes are numbered, but a few are not. The abbreviations “X” and “Y” refer to the human sex chromosomes. a. How many different types of chromosomes do you see? b. What does “MT” represent? [Note: you can click the “MT” link to find out.] c. With the exception of MT, the chromosomes of the human genome are in pairs. X and Y are a pair. Using this information and the information from your answer to Question 9A, how many pairs of chromosomes are in the human genome? 10. The Breast Cancer Susceptibility gene BRCA1 is on chromosome 17 in humans. [Click on the link below chromosome 17.] Explore some of the links and views. What do you see when you click on chromosome 17? Explore some of the links on the picture, and write down two things you found interesting, such as the description of other genes that are also found on chromosome 17. 11. To find the location of the BRCA1 gene, type “BRCA1” in the “Search” box at the top left of the screen, and click “Find in This View.” Scroll through the Map of Chromosome 17 and locate the BRCA1 gene, which should be highlighted in pink. “BRCA1” will be found in the list of Symbols. You can also use the “Find” feature (PC: “Control+F” Mac: “Command+F”), which will highlight in yellow every mention of “BRCA1,” including the BRCA1 gene. Draw a picture of chromosome 17 and show the approximate location of BRCA1 on this chromosome. Figure 5: Find the location of the BRCA1 gene by using the search function. Credit: NCBI. 12. Click on the BRCA1 link. This will take you to Entrez Gene, which provides a summary of the information available at the NCBI for BRCA1. Scroll through the webpage and explore some of the information available. Scroll down the webpage to the section titled “Gene Ontology.” There is a table titled “Function.” List three of the functions that the BRCA1 protein performs. Figure 6: Click on the “BRCA1” link to launch Entrez Gene. Credit: NCBI. Figure 7: S_c_r_o_l_l_ _d_o_w_n_ _t_o_ _f_i_n_d_ _t_h_e_ _“G_e_n_e_ _O_n_t_o_l_o_g_y_” _s_e_c_t_i_o_n_. Figure 8: S_e_l_e_c_t_ _“P_h_e_n_o_t_y_p_e_s_” _f_r_o_m_ _t_h_e_ _T_a_b_l_e_ _o_f_ _C_o_n_t_e_n_t_s. 13. To learn about all of the phenotypes associated with mutations of BRCA1, return to the top of the web page and from the “Table of Contents” on the right, select “Phenotypes.” This will bring you to the portion of the web page that contains the phenotype information for BRCA1. a. Based on what you’ve learned in class, what is a phenotype? b_._ _W_h_a_t_ _phenotypes a_r_e_ _a_s_s_o_c_i_a_t_e_d_ _w_i_t_h_ _m_u_t_a_t_i_o_n_s_ _i_n_ _t_h_e_ _BRCA1 g_e_n_e_?_ _(_Y_o_u_ _d_o_n_’t_ _n_e_e_d_ _t_o_ _c_l_i_c_k_ _t_h_e_ _l_i_n_k_s_._)_ _ 14. Return to the Table of Contents at the top of the page and click “Reference Sequences.” This will take you to the portion of the webpage that contains the actual genetic sequence of the BRCA1 gene. 15 Reference sequences a_r_e_ _D_N_A_ _o_r_ _p_r_o_t_e_i_n_ _s_e_q_u_e_n_c_e_s_ _t_h_a_t_ _s_c_i_e_n_t_i_s_t_s_,_ _d_o_c_t_o_r_s_ _a_n_d_ _g_e_n_e_t_i_c_ _c_o_u_n_s_e_l_o_r_s_ _u_s_e_ _t_o_ _s_t_u_d_y_ _g_e_n_e_s_ _l_i_k_e_ _BRCA1._ _Y_o_u_ _c_a_n_ _d_o_w_n_l_o_a_d_ _t_h_e_s_e_ _s_e_q_u_e_n_c_e_s_ _i_n_ _d_i_f_f_e_r_e_n_t_ _f_o_r_m_a_t_s_._ _F_o_r_ _t_h_i_s_ _e_x_e_r_c_i_s_e_,_ _c_l_i_c_k_ _“FASTA” _(_w_h_i_c_h_ _i_s_ _s_o_m_e_t_i_m_e_s_ _p_r_o_n_o_u_n_c_e_d_ _F_A_S_T_-_a_y_)_._ _ Figure 9: Click “FASTA” to obtain the FASTA sequence for BRCA1. Credit: NCBI. Figure 10: Take a look at the FASTA sequence for BRCA1. Credit: NCBI. 16. This link takes you to the FASTA sequence for BRCA1. Scroll through the web page. This gene is very large! a. What four letters make up this long sequence? b. Based on what you’ve learned in class, what do these letters represent? 17. Return to the NCBI homepage by clicking on the NCBI icon on the top left of the web page. Figure 11: Return to the NCBI homepage by clicking on the logo. Credit: NCBI. 18 T_y_p_e_ _BRCA1 i_n_ _t_h_e_ _Search b_o_x_ _a_n_d_ _s_e_l_e_c_t_ _“Nucleotide” _f_r_o_m_ _t_h_e_ _p_u_l_l_-_d_o_w_n_ _m_e_n_u_ _b_e_s_i_d_e_ _t_h_e_ _Search b_o_x_,_ _t_o_ _l_i_m_i_t_ _y_o_u_r_ _s_e_a_r_c_h_ _t_o_ _t_h_e_ _d_a_t_a_b_a_s_e_ _c_o_n_t_a_i_n_i_n_g_ _a_l_l_ _o_f_ _t_h_e_ _D_N_A_ _a_n_d_ _R_N_A_ _(_N_u_c_l_e_o_t_i_d_e_)_ _s_e_q_u_e_n_c_e_s_._ _C_l_i_c_k_ _t_h_e_ _“S_e_a_r_c_h_” _b_u_t_t_o_n_._ _ Figure 12: T_y_p_e_ _“B_R_C_A_1_” _i_n_t_o_ _t_h_e_ _S_e_a_r_c_h_ _b_o_x_ _a_n_d_ _c_h_o_o_s_e_ _“N_u_c_l_e_o_t_i_d_e_” _f_r_o_m_ _t_h_e_ _p_u_l_l_-_d_o_w_n_ _m_e_n_u_._ _C_r_e_d_i_t_:_ _N_C_B_I_._ 19. What other organisms have BRCA1 genes? You can scroll through the list of organisms, but note that these are listed by the scientific name of the organism (Genus and species), not the common name. For example, Homo sapiens is the scientific name for humans. Also, the Top Organisms (or the organisms with the most “hits”) are listed on the right. Helpful Hint: Hold your cursor over the species name to see the common name appear. Alternatively, you can perform an internet search to find the common name(s) of your organisms. List three organisms other than humans that have BRCA1 genes. Include both the scientific and common names. Figure 13: Scroll through the list of Top Organisms. Credit: NCBI 20. Look back at your list of functions for the BRCA1 gene (question #12). Does it surprise you that so many organisms share the BRCA1 gene? Explain. 21. What kind of information can you find at the National Center for Biotechnology Information? Summarize what you have learned today by listing three types of information found at the NCBI